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## P

PaletteColor - Class in org.metaqtl.graph
PaletteColor() - Constructor for class org.metaqtl.graph.PaletteColor
parent - Variable in class org.metaqtl.TreeNode
  The parent of the node
parents - Variable in class org.thalia.bio.entity.Population
parse(String[]) - Method in class org.metaqtl.main.CmdLineParser
  Extract the options and non-option arguments from the given list of command-line arguments.
parse(String[], Locale) - Method in class org.metaqtl.main.CmdLineParser
  Extract the options and non-option arguments from the given list of command-line arguments.
parseChromList(String) - Static method in class org.metaqtl.main.MetaMain
parseCmdLine(String[]) - Method in class org.metaqtl.main.MetaMain
parseCross(String) - Static method in class org.thalia.bio.util.BioCrossTypes
  Parse the given string and return if valid the type of cross and the number of generations.
parseDouble(String) - Static method in class org.thalia.bio.util.NumberFormat
  This method parse the given string to a double value.
parseType(String) - Static method in class org.thalia.bio.util.BioLocusTypes
pi - Variable in class org.metaqtl.EMResult
  The mixing proportions.
pnames - Variable in class org.metaqtl.QtlPartition
  The partition names.
Population - Class in org.thalia.bio.entity
  Class Description Here
Population() - Constructor for class org.thalia.bio.entity.Population
Population(String, IBioEntity) - Constructor for class org.thalia.bio.entity.Population
POPULATION - Static variable in interface org.thalia.bio.IBioEntityTypes
  The integer code for Population entity
POS_COMMON - Static variable in class org.metaqtl.graph.ChromLayer
POS_COMMON_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
position - Variable in class org.metaqtl.Qtl
  The QTL most probable location on the chromosome.
position - Variable in class org.thalia.bio.entity.bean.LocusBean
printHelp() - Method in class org.metaqtl.main.A2Xml
printHelp() - Method in class org.metaqtl.main.ConsMap
printHelp() - Method in class org.metaqtl.main.InfoMap
printHelp() - Method in class org.metaqtl.main.MapView
printHelp() - Method in class org.metaqtl.main.MetaDB
printHelp() - Method in class org.metaqtl.main.MetaMain
printHelp() - Method in class org.metaqtl.main.MMapView
printHelp() - Method in class org.metaqtl.main.MQTLView
printHelp() - Method in class org.metaqtl.main.QTLClust
printHelp() - Method in class org.metaqtl.main.QTLClustInfo
printHelp() - Method in class org.metaqtl.main.QTLModel
printHelp() - Method in class org.metaqtl.main.QTLProj
printHelp() - Method in class org.metaqtl.main.QTLTree
printHelp() - Method in class org.metaqtl.main.Xml2A
printHelp() - Method in class org.thalia.metaqtl.main.MetaCMS
printHelp() - Method in class org.thalia.metaqtl.main.MetaDraw
printHelp() - Method in class org.thalia.metaqtl.main.MetaMapDraw
printHelp() - Method in class org.thalia.metaqtl.main.MetaSimu
printHelp() - Method in class org.thalia.metaqtl.main.MetaSimuStat
printImgFormat(int) - Static method in class org.metaqtl.main.MetaMain
printLicense(String, String) - Static method in class org.metaqtl.main.MetaMain
printUsage() - Method in class org.metaqtl.main.A2Xml
printUsage() - Method in class org.metaqtl.main.ConsMap
printUsage() - Method in class org.metaqtl.main.InfoMap
printUsage() - Method in class org.metaqtl.main.MapView
printUsage() - Method in class org.metaqtl.main.MetaDB
printUsage() - Method in class org.metaqtl.main.MetaMain
printUsage() - Method in class org.metaqtl.main.MMapView
printUsage() - Method in class org.metaqtl.main.MQTLView
printUsage() - Method in class org.metaqtl.main.QTLClust
printUsage() - Method in class org.metaqtl.main.QTLClustInfo
printUsage() - Method in class org.metaqtl.main.QTLModel
printUsage() - Method in class org.metaqtl.main.QTLProj
printUsage() - Method in class org.metaqtl.main.QTLTree
printUsage() - Method in class org.metaqtl.main.Xml2A
printUsage() - Method in class org.thalia.metaqtl.main.MetaCMS
printUsage() - Method in class org.thalia.metaqtl.main.MetaDraw
printUsage() - Method in class org.thalia.metaqtl.main.MetaMapDraw
printUsage() - Method in class org.thalia.metaqtl.main.MetaSimu
printUsage() - Method in class org.thalia.metaqtl.main.MetaSimuStat
proba - Variable in class org.metaqtl.Chromosome
  Probabilities defined along the chromosome.
proba - Variable in class org.metaqtl.QtlPartition
  The probabilities of each Qtl to belong to each partition.
PROBA_BIN - Static variable in class org.metaqtl.graph.MetaGraphPar
PROBA_FROM_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
PROBA_PALETTE - Static variable in class org.metaqtl.graph.MetaGraphPar
PROBA_TO_COLOR - Static variable in class org.metaqtl.graph.MetaGraphPar
proj - Variable in class org.metaqtl.Qtl
  The QTL projection properties.
properties - Variable in class org.thalia.bio.entity.bean.BioEntityBean
PropertyBean - Class in org.thalia.bio.entity.bean
  Class Description Here
PropertyBean() - Constructor for class org.thalia.bio.entity.bean.PropertyBean
PropertyBean(String, String) - Constructor for class org.thalia.bio.entity.bean.PropertyBean
PVALUE - Static variable in interface org.metaqtl.IBioLGroupProperties
  The key for the p-value.
pvalue - Variable in class org.metaqtl.MetaChrom
  The p-value of this chromosome.
pvalue - Variable in class org.metaqtl.MultiFitResult
  The p-value of the model.
PYTHAG(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Computes sqrt(a^2+b^2)

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